assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCA_003855135.1_ASM385513v1	CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	1	972453-972554	1	CRISPRCasFinder	no		cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	Orphan	TTGTTGATGTTGTTGTGTTTTGTA	24	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	NA,NA|55aa|down_0|CP034060.1_972594_972759_-	NA|115aa|up_9|CP034060.1_960124_960469_-	PRK11424, PRK11424, DNA-binding transcriptional activator TdcR; Provisional	NA|313aa|up_8|CP034060.1_960658_961597_+	PRK10341, PRK10341, transcriptional regulator TdcA	NA|330aa|up_7|CP034060.1_961695_962685_+	PRK08638, PRK08638, bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB	NA|444aa|up_6|CP034060.1_962706_964038_+	PRK13629, PRK13629, threonine/serine transporter TdcC; Provisional	NA|403aa|up_5|CP034060.1_964063_965272_+	PRK12379, PRK12379, propionate kinase	NA|765aa|up_4|CP034060.1_965305_967600_+	cd01678, PFL1, Pyruvate formate lyase 1	NA|130aa|up_3|CP034060.1_967613_968003_+	PRK11401, PRK11401, enamine/imine deaminase	NA|455aa|up_2|CP034060.1_968074_969439_+	PRK15040, PRK15040, L-serine ammonia-lyase	NA|444aa|up_1|CP034060.1_969713_971045_+	TIGR00814, membrane_transport_protein_YhjV, serine transporter	NA|437aa|up_0|CP034060.1_971072_972383_+	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|55aa|down_0|CP034060.1_972594_972759_-	NA	NA|234aa|down_1|CP034060.1_972781_973483_-	COG1741, COG1741, Pirin-related protein [General function prediction only]	NA|299aa|down_2|CP034060.1_973587_974484_+	cd08431, PBP2_HupR, The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold	NA|123aa|down_3|CP034060.1_975467_975836_-	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|329aa|down_4|CP034060.1_976128_977115_-	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]	NA|129aa|down_5|CP034060.1_977184_977571_-	COG2259, COG2259, Predicted membrane protein [Function unknown]	NA|100aa|down_6|CP034060.1_977666_977966_-	pfam13997, YqjK, YqjK-like protein	NA|135aa|down_7|CP034060.1_977955_978360_-	COG5393, COG5393, Predicted membrane protein [Function unknown]	NA|102aa|down_8|CP034060.1_978362_978668_-	COG4575, ElaB, Uncharacterized conserved protein [Function unknown]	NA|128aa|down_9|CP034060.1_979206_979590_-	PRK10629, PRK10629, EnvZ/OmpR regulon moderator MzrA
GCA_003855135.1_ASM385513v1	CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	2	1075920-1076085	2	CRISPRCasFinder	no		cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	Orphan	ATCAGGCCTACAAAATCTATTGCAACATGTTGAATCTTCGTGCGTTTGTAGGC	53	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	NA,NA	NA|740aa|up_9|CP034060.1_1065563_1067783_+	PRK01254, PRK01254, YgiQ family radical SAM protein	NA|86aa|up_8|CP034060.1_1067825_1068083_-	PRK09973, PRK09973, lipoprotein YqhH	NA|309aa|up_7|CP034060.1_1068133_1069060_-	pfam12883, DUF3828, Protein of unknown function (DUF3828)	NA|276aa|up_6|CP034060.1_1069259_1070087_-	PRK11565, dkgA, 2,5-didehydrogluconate reductase DkgA	NA|388aa|up_5|CP034060.1_1070191_1071355_-	PRK15138, PRK15138, alcohol dehydrogenase	NA|319aa|up_4|CP034060.1_1071491_1072448_+	pfam06719, AraC_N, AraC-type transcriptional regulator N-terminus	NA|220aa|up_3|CP034060.1_1072487_1073147_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|396aa|up_2|CP034060.1_1073286_1074474_-	PRK08114, PRK08114, cystathionine beta-lyase; Provisional	NA|245aa|up_1|CP034060.1_1074725_1075460_+	PRK10414, PRK10414, biopolymer transporter ExbB	NA|142aa|up_0|CP034060.1_1075466_1075892_+	PRK11267, PRK11267, biopolymer transport protein ExbD; Provisional	NA|295aa|down_0|CP034060.1_1076163_1077048_-	PRK07985, PRK07985, SDR family oxidoreductase	NA|165aa|down_1|CP034060.1_1077238_1077733_+	PRK05208, PRK05208, hypothetical protein; Provisional	NA|347aa|down_2|CP034060.1_1077772_1078813_-	PRK09912, PRK09912, L-glyceraldehyde 3-phosphate reductase; Provisional	NA|296aa|down_3|CP034060.1_1078969_1079857_+	COG0412, COG0412, Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]	NA|96aa|down_4|CP034060.1_1079975_1080263_+	pfam11115, DUF2623, Protein of unknown function (DUF2623)	NA|373aa|down_5|CP034060.1_1080451_1081570_+	PRK10468, PRK10468, hydrogenase 2 small subunit; Provisional	NA|329aa|down_6|CP034060.1_1081572_1082559_+	PRK10882, PRK10882, hydrogenase 2 operon protein HybA	NA|393aa|down_7|CP034060.1_1082548_1083727_+	PRK10881, PRK10881, Ni/Fe-hydrogenase cytochrome b subunit	NA|568aa|down_8|CP034060.1_1083723_1085427_+	PRK10467, PRK10467, hydrogenase 2 large subunit; Provisional	NA|165aa|down_9|CP034060.1_1085426_1085921_+	PRK10466, hybD, HyaD/HybD family hydrogenase maturation endopeptidase
GCA_003855135.1_ASM385513v1	CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	3	1808830-1808947	3	CRISPRCasFinder	no		cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	Orphan	CCGAGCCGTAGGCCGGATAAGGCGTTCACGC	31	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	NA,NA	NA|317aa|up_9|CP034060.1_1796926_1797877_-	PRK09956, PRK09956, ISNCY family transposase	NA|397aa|up_8|CP034060.1_1798069_1799260_-	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|420aa|up_7|CP034060.1_1799256_1800516_-	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|543aa|up_6|CP034060.1_1800505_1802134_-	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|453aa|up_5|CP034060.1_1802406_1803765_+	PRK11273, glpT, glycerol-3-phosphate transporter	NA|359aa|up_4|CP034060.1_1803769_1804846_+	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|425aa|up_3|CP034060.1_1805153_1806427_+	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|217aa|up_2|CP034060.1_1806644_1807295_+	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|85aa|up_1|CP034060.1_1807348_1807603_-	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|377aa|up_0|CP034060.1_1807602_1808733_-	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|762aa|down_0|CP034060.1_1808966_1811252_-	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|425aa|down_1|CP034060.1_1812138_1813412_-	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|552aa|down_2|CP034060.1_1813430_1815086_+	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|645aa|down_3|CP034060.1_1815095_1817030_+	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|241aa|down_4|CP034060.1_1817157_1817880_-	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|876aa|down_5|CP034060.1_1818026_1820654_+	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|208aa|down_6|CP034060.1_1822487_1823111_+	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|390aa|down_7|CP034060.1_1825458_1826627_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|550aa|down_8|CP034060.1_1828901_1830551_+	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|259aa|down_9|CP034060.1_1830555_1831332_+	COG4676, COG4676, Uncharacterized protein conserved in bacteria [Function unknown]
GCA_003855135.1_ASM385513v1	CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	4	2442642-2442765	4	CRISPRCasFinder	no	c2c9_V-U4,DEDDh	cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	Unclear	CGACCCCCACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA	43	0	0	NA	NA	NA	1	1	Unclear	cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	NA,NA|30aa|down_7|CP034060.1_2451661_2451751_+	NA|471aa|up_9|CP034060.1_2431320_2432733_-	PRK09206, PRK09206, pyruvate kinase PykF	NA|70aa|up_8|CP034060.1_2434065_2434275_+	PRK10292, PRK10292, fumarate hydratase FumD	NA|209aa|up_7|CP034060.1_2434730_2435357_+	PRK09898, PRK09898, ferredoxin-like protein	NA|103aa|up_6|CP034060.1_2435377_2435686_+	PRK09849, PRK09849, putative oxidoreductase; Provisional	NA|216aa|up_5|CP034060.1_2437482_2438130_+	PRK09947, PRK09947, YdhW family putative oxidoreductase system protein	NA|223aa|up_4|CP034060.1_2438193_2438862_+	TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein	NA|262aa|up_3|CP034060.1_2438858_2439644_+	PRK15006, PRK15006, thiosulfate reductase cytochrome B subunit; Provisional	NA|271aa|up_2|CP034060.1_2439647_2440460_+	PRK09946, PRK09946, hypothetical protein; Provisional	NA|535aa|up_1|CP034060.1_2440471_2442076_-	PRK09897, PRK09897, FAD-NAD(P)-binding protein	NA|102aa|up_0|CP034060.1_2442201_2442507_-	PRK11118, PRK11118, putative monooxygenase; Provisional	NA|419aa|down_0|CP034060.1_2443079_2444336_+	PRK09945, PRK09945, hypothetical protein; Provisional	NA|458aa|down_1|CP034060.1_2444376_2445750_-	PRK01766, PRK01766, multidrug efflux protein; Reviewed	NA|214aa|down_2|CP034060.1_2445964_2446606_+	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional	NA|383aa|down_3|CP034060.1_2446645_2447794_-	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase	NA|404aa|down_4|CP034060.1_2448084_2449296_-	PRK11043, PRK11043, Bcr/CflA family multidrug efflux MFS transporter	NA|311aa|down_5|CP034060.1_2449408_2450341_+	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional	NA|342aa|down_6|CP034060.1_2450337_2451363_-	PRK10703, PRK10703, HTH-type transcriptional repressor PurR	NA|30aa|down_7|CP034060.1_2451661_2451751_+	NA	NA|390aa|down_8|CP034060.1_2451916_2453086_+	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]	NA|194aa|down_9|CP034060.1_2453231_2453813_-	PRK10543, PRK10543, superoxide dismutase [Fe]
GCA_003855135.1_ASM385513v1	CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	5	3347625-3347773	5,1	CRISPRCasFinder,PILER-CR	no		cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	Orphan	ATTTCTAAGCTGCCTGTACGGCAGTGAAC,ATTTCTAAGCTGCCTGTACGGCAGTGAAC	29,29	0	0	NA	NA	I-F:I-F	2,2	2	Orphan	cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	NA,NA	NA|431aa|up_9|CP034060.1_3332711_3334004_-	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional	NA|448aa|up_8|CP034060.1_3334094_3335438_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|204aa|up_7|CP034060.1_3335448_3336060_-	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|1343aa|up_6|CP034060.1_3336214_3340243_-	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|165aa|up_5|CP034060.1_3340377_3340872_-	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|322aa|up_4|CP034060.1_3341415_3342381_+	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|589aa|up_3|CP034060.1_3342503_3344270_+	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|574aa|up_2|CP034060.1_3344270_3345992_+	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|235aa|up_1|CP034060.1_3346033_3346738_+	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|73aa|up_0|CP034060.1_3347022_3347241_+	PRK00276, infA, translation initiation factor IF-1; Validated	NA|759aa|down_0|CP034060.1_3347984_3350261_-	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|107aa|down_1|CP034060.1_3350291_3350612_-	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|75aa|down_2|CP034060.1_3350934_3351159_+	PRK09937, PRK09937, cold shock-like protein CspD	NA|649aa|down_3|CP034060.1_3351231_3353178_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|372aa|down_4|CP034060.1_3353174_3354290_-	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|331aa|down_5|CP034060.1_3354404_3355397_+	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|553aa|down_6|CP034060.1_3355393_3357052_-	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|232aa|down_7|CP034060.1_3358252_3358948_+	PRK05420, PRK05420, aquaporin Z; Provisional	NA|300aa|down_8|CP034060.1_3359404_3360304_+	COG2431, COG2431, Predicted membrane protein [Function unknown]	NA|551aa|down_9|CP034060.1_3360447_3362100_+	PRK05290, PRK05290, hybrid cluster protein; Provisional
GCA_003855135.1_ASM385513v1	CP034060	Shigella flexneri strain FDAARGOS_535 chromosome, complete genome	6	4141690-4141805	6	CRISPRCasFinder	no		cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	Orphan	AACGCCTGATGCGACGCTGACGCGTCTTATC	31	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol	NA,NA	NA|393aa|up_9|CP034060.1_4129705_4130884_-	TIGR00899, Sugar_efflux_transporter_A, sugar efflux transporter	NA|44aa|up_8|CP034060.1_4130985_4131117_-	pfam15894, SgrT, Inhibitor of glucose uptake transporter SgrT	NA|552aa|up_7|CP034060.1_4131205_4132861_+	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|328aa|up_6|CP034060.1_4133024_4134008_+	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|537aa|up_5|CP034060.1_4133983_4135594_+	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|233aa|up_4|CP034060.1_4135577_4136276_+	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|255aa|up_3|CP034060.1_4136389_4137154_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|293aa|up_2|CP034060.1_4137239_4138118_-	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|567aa|up_1|CP034060.1_4138456_4140157_+	PRK04123, PRK04123, ribulokinase; Provisional	NA|501aa|up_0|CP034060.1_4140167_4141670_+	PRK02929, PRK02929, L-arabinose isomerase; Provisional	NA|232aa|down_0|CP034060.1_4141869_4142565_+	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|784aa|down_1|CP034060.1_4142639_4144991_+	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|969aa|down_2|CP034060.1_4145155_4148062_+	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|220aa|down_3|CP034060.1_4148073_4148733_+	PRK10158, PRK10158, bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA|272aa|down_4|CP034060.1_4148849_4149665_-	PRK09430, djlA, co-chaperone DjlA	NA|785aa|down_5|CP034060.1_4149919_4152274_+	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|429aa|down_6|CP034060.1_4152326_4153613_+	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|330aa|down_7|CP034060.1_4153612_4154602_+	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|274aa|down_8|CP034060.1_4154598_4155420_+	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|126aa|down_9|CP034060.1_4155422_4155800_+	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed
